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// ______ ______ _ _ _____ ______ |
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// | ____| ____| | (_)/ ____| | ____| |
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// | |__ | |__ | | _| (___ ___| |__ |
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// | __| | __| | | | |\___ \ / __| __| |
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// | | | |____| |____| |____) | (__| |____ |
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// |_| |______|______|_|_____/ \___|______| |
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// Finite Elements for Life Sciences and Engineering |
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// |
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// License: LGL2.1 License |
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// FELiScE default license: LICENSE in root folder |
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// |
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// Main authors: A. Collin |
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// |
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// System includes |
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// External includes |
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// Project includes |
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#include "Model/bidomainCurvModel.hpp" |
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namespace felisce { |
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BidomainCurvModel::BidomainCurvModel(): |
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Model(), |
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m_ionic(nullptr), |
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m_schaf(nullptr), |
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m_fhn(nullptr), |
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m_court(nullptr), |
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m_buildIonic(false), |
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m_buildCourt(false), |
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m_verbose(0) { |
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for(std::size_t i=0; i<m_linearProblemBidomainCurv.size(); i++) { |
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m_linearProblemBidomainCurv[i] = nullptr; |
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} |
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m_name = "BidomainCurv"; |
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} |
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BidomainCurvModel::~BidomainCurvModel() { |
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for(std::size_t i=0; i<m_linearProblemBidomainCurv.size(); i++) { |
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m_linearProblemBidomainCurv[i] = nullptr; |
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} |
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if (m_buildIonic) { |
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delete m_ionic; |
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m_ionic = nullptr; |
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} |
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if (m_buildCourt) { |
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delete m_court; |
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m_court = nullptr; |
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} |
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m_solExtraCell.destroy(); |
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m_extrapolate.destroy(); |
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if (m_buildCourt) { |
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m_m.destroy(); |
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m_h.destroy(); |
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m_j.destroy(); |
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m_ao.destroy(); |
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m_io.destroy(); |
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m_ua.destroy(); |
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m_ui.destroy(); |
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m_xr.destroy(); |
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m_xs.destroy(); |
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m_d.destroy(); |
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m_f.destroy(); |
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m_fca.destroy(); |
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m_urel.destroy(); |
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m_vrel.destroy(); |
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m_wrel.destroy(); |
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m_nai.destroy(); |
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m_nao.destroy(); |
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m_cao.destroy(); |
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m_ki.destroy(); |
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m_ko.destroy(); |
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m_cai.destroy(); |
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m_naiont.destroy(); |
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m_kiont.destroy(); |
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m_caiont.destroy(); |
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m_ileak.destroy(); |
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m_iup.destroy(); |
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m_itr.destroy(); |
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m_irel.destroy(); |
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m_cmdn.destroy(); |
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m_trpn.destroy(); |
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m_nsr.destroy(); |
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m_jsr.destroy(); |
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m_csqn.destroy(); |
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} else { |
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m_W_0.destroy(); |
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} |
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delete m_iApp; |
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if (FelisceParam::instance().hasAppliedExteriorCurrent) |
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delete m_iAppExt; |
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} |
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void BidomainCurvModel::initializeDerivedLinearProblem() { |
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for (std::size_t i=0; i<m_linearProblem.size(); i++) { |
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m_linearProblemBidomainCurv.push_back(static_cast<LinearProblemBidomainCurv*>(m_linearProblem[i])); |
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} |
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} |
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//! Define m_schaf and m_bdfEdp (use in linearProblem). |
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void BidomainCurvModel::initializeDerivedModel() { |
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m_verbose = FelisceParam::verbose(); |
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if (FelisceParam::instance().typeOfIonicModel == "schaf") { |
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//Allocate m_schaf. |
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m_schaf = new SchafSolver(m_fstransient); |
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m_ionic = m_schaf; |
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//Fix order of bdf for schaf solver. |
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m_schaf->defineOrderBdf(FelisceParam::instance().orderBdfIonic); |
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} else if (FelisceParam::instance().typeOfIonicModel == "fhn") { |
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// Initialize Fitzhugh-Nagumo model |
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m_fhn = new FhNSolver(m_fstransient); |
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m_ionic =m_fhn; |
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m_ionic->defineOrderBdf(FelisceParam::instance().orderBdfIonic,1); |
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} else if (FelisceParam::instance().typeOfIonicModel == "court") { |
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//Allocate m_court. |
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m_court = new CourtemancheSolver(m_fstransient); |
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} |
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//Define order for bdf used by EDP (linearProblem). |
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m_bdfEdp.defineOrder(FelisceParam::instance().orderBdfEdp); |
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initializeAppCurrent(); |
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if (FelisceParam::instance().hasAppliedExteriorCurrent) |
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initializeAppCurrentExt(); |
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} |
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void BidomainCurvModel::setInitialCondition() { |
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for (std::size_t iProblem=0; iProblem<m_linearProblemBidomainCurv.size(); iProblem++) { |
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m_U_0.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
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m_U_0.set(0.0); |
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if (FelisceParam::instance().hasInitialCondition) { |
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int idVar = -1; |
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double valueByDofU_0; |
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for (std::size_t iListVar = 0; iListVar < m_initialCondition.listVariable().size(); iListVar++) { |
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for ( std::size_t iUnknown = 0; iUnknown < m_linearProblemBidomainCurv[iProblem]->listUnknown().size(); iUnknown++) { |
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idVar = m_linearProblemBidomainCurv[iProblem]->listUnknown().idVariable(iUnknown); |
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if ( m_linearProblemBidomainCurv[iProblem]->listVariable()[idVar].name() == m_initialCondition.listVariable()[iListVar].name() ) { |
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felInt numDofLpU = m_linearProblemBidomainCurv[iProblem]->numDofLocalPerUnknown(m_linearProblemBidomainCurv[iProblem]->listUnknown()[iUnknown]); |
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felInt idLocalValue[numDofLpU]; |
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felInt idGlobalValue[numDofLpU]; |
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for ( felInt ii = 0; ii < numDofLpU; ii++) { |
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idLocalValue[ii] = ii; |
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} |
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ISLocalToGlobalMappingApply(m_linearProblemBidomainCurv[iProblem]->mappingDofLocalToDofGlobal(m_linearProblemBidomainCurv[iProblem]->listUnknown()[iUnknown]),numDofLpU,&idLocalValue[0],&idGlobalValue[0]); |
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if (idVar==0) { |
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for (felInt ii = 0; ii < numDofLpU; ii++) { |
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valueByDofU_0 = FelisceParam::instance().valueInitCond[iListVar]; |
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m_U_0.setValue(idGlobalValue[ii],valueByDofU_0,INSERT_VALUES);; |
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} |
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} else if (idVar==1) { |
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for (felInt ii = 0; ii < numDofLpU; ii++) { |
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if (ii < static_cast<int>(numDofLpU/2)) { |
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valueByDofU_0 = 0.0; |
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} else { |
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valueByDofU_0 = 0.0; |
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} |
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m_U_0.setValue(idGlobalValue[ii],valueByDofU_0,INSERT_VALUES); |
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} |
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} |
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} |
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} |
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} |
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} |
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m_U_0.assembly(); |
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//Initialize solution for solver. |
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m_linearProblemBidomainCurv[iProblem]->solution().copyFrom(m_U_0); |
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} |
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} |
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void BidomainCurvModel::initializeAppCurrent() { |
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m_iApp = new AppCurrentAtria(); |
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m_iApp->initialize(m_fstransient); |
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} |
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void BidomainCurvModel::initializeAppCurrentExt() { |
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m_iAppExt = new AppCurrentAtria(); |
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m_iAppExt->initialize(m_fstransient); |
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} |
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void BidomainCurvModel::evalIapp() { |
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m_iAppValue.clear(); |
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m_linearProblemBidomainCurv[0]->evalFunctionOnDof(*m_iApp,m_fstransient->time,m_iAppValue); |
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} |
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void BidomainCurvModel::evalIappExt() { |
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m_iAppValueExt.clear(); |
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m_linearProblemBidomainCurv[0]->evalFunctionOnDof(*m_iAppExt,m_fstransient->time,m_iAppValueExt); |
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} |
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void BidomainCurvModel::finalizeRHSDP(std::size_t iProblem) { |
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int size = m_linearProblemBidomainCurv[iProblem]->numDofLocalPerUnknown(potTransMemb); |
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double valueForPetsc[size]; |
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felInt idLocalValue[size]; |
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felInt idGlobalValue[size]; |
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double coefAm = FelisceParam::instance().Am; |
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double coefCm = FelisceParam::instance().Cm; |
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// RHS = Am*Cm*BDF.RHS (Warning : bdf.RHS containes both problem variables). |
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m_linearProblemBidomainCurv[iProblem]->vector().axpy(1.,m_bdfEdp.vector()); |
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m_linearProblemBidomainCurv[iProblem]->vector().scale(coefAm*coefCm); |
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// RHS = RHS + Am*Iapp |
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for (felInt i = 0; i < size; i++) { |
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idLocalValue[i] = i; |
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} |
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ISLocalToGlobalMappingApply(m_linearProblemBidomainCurv[iProblem]->mappingDofLocalToDofGlobal(potTransMemb),size,&idLocalValue[0],&idGlobalValue[0]); |
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for (felInt i = 0; i < size; i++) { |
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felInt indexGlobal=idGlobalValue[i]; |
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valueForPetsc[i] = coefAm*m_iAppValue[indexGlobal]; |
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} |
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m_linearProblemBidomainCurv[iProblem]->vector().setValues(size,&idGlobalValue[0],&valueForPetsc[0],ADD_VALUES); |
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m_linearProblemBidomainCurv[iProblem]->vector().assembly(); |
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// For the second equation : RHS = 0 ( or applied exterior current ) |
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int sizePotExtraCell = m_linearProblemBidomainCurv[iProblem]->numDofLocalPerUnknown(potExtraCell); |
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double valueForPetscPotExtraCell[sizePotExtraCell]; |
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felInt idLocalValuePotExtraCell[sizePotExtraCell]; |
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felInt idGlobalValuePotExtraCell[sizePotExtraCell]; |
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for (felInt i = 0; i < sizePotExtraCell; i++) { |
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idLocalValuePotExtraCell[i] = i; |
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} |
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ISLocalToGlobalMappingApply(m_linearProblemBidomainCurv[iProblem]->mappingDofLocalToDofGlobal(potExtraCell),sizePotExtraCell,&idLocalValuePotExtraCell[0],&idGlobalValuePotExtraCell[0]); |
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for (felInt i = 0; i < sizePotExtraCell; i++) { |
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// For an applied exterior current |
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if (FelisceParam::instance().hasAppliedExteriorCurrent) { |
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valueForPetscPotExtraCell[i] = m_iAppValueExt[idGlobalValuePotExtraCell[i]]; |
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} else { |
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valueForPetscPotExtraCell[i] = 0.0; |
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} |
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} |
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m_linearProblemBidomainCurv[iProblem]->vector().setValues(sizePotExtraCell ,&idGlobalValuePotExtraCell[0],&valueForPetscPotExtraCell[0],INSERT_VALUES); |
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m_linearProblemBidomainCurv[iProblem]->vector().assembly(); |
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if (FelisceParam::instance().typeOfIonicModel == "court") { |
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m_linearProblemBidomainCurv[0]->vector().axpy(-coefAm*coefCm,m_court->ion()); |
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} else { |
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m_linearProblemBidomainCurv[0]->vector().axpy(coefAm,m_ionic->ion()); |
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} |
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// Elisa, Dec. 2014 - Luenberger filter |
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if (FelisceParam::instance().electrodeControl) { |
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m_linearProblemBidomainCurv[iProblem]->addElectrodeCondtrol(); |
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} |
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} |
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void BidomainCurvModel::preAssemblingMatrixRHS(std::size_t iProblem) { |
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//Initialize std::vector useful (with m_W_0) with a std::vector with same structure as _RHS in linearProblem. |
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| 263 |
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// 1) copy structure in m_W_0 (initialize solution at time 0 of EDO in schaf solver). |
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m_W_0.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
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m_W_0.zeroEntries(); |
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| 267 |
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// 2) copy structure in m_extrapolate (contains extrapolate values of linearProblem solution). |
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m_extrapolate.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
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m_extrapolate.zeroEntries(); |
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m_solExtraCell.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
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m_solExtraCell.zeroEntries(); |
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if (FelisceParam::instance().typeOfIonicModel == "schaf") { |
| 275 |
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double valueByDofW_0 = 1./((FelisceParam::instance().vMax - FelisceParam::instance().vMin)*(FelisceParam::instance().vMax - FelisceParam::instance().vMin)); |
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m_W_0.set(valueByDofW_0); |
| 277 |
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} |
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if (FelisceParam::instance().typeOfIonicModel == "court") { |
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double valueByDofm = 0.00291; |
| 282 |
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double valueByDofh = 0.965; |
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double valueByDofj = 0.978; |
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double valueByDofao = 0.0304; |
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double valueByDofio = 0.999; |
| 286 |
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double valueByDofua = 0.00496; |
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double valueByDofui = 0.999; |
| 288 |
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double valueByDofxr = 0.0000329; |
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double valueByDofxs = 0.0187; |
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double valueByDofd = 0.000137; |
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double valueByDoff = 0.999837; |
| 292 |
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double valueByDoffca = 0.775; |
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double valueByDofvrel = 1.00; |
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double valueByDofwrel = 0.999; |
| 295 |
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double valueByDofnai = 11.2; |
| 296 |
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double valueByDofnao = 140.0; |
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double valueByDofcao = 1.8; |
| 298 |
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double valueByDofki = 139.0; |
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double valueByDofko = 4.5; |
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double valueByDofcai = 0.000102; |
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double valueByDofcmdn = 0.00205; |
| 302 |
|
✗ |
double valueByDoftrpn = 0.0118; |
| 303 |
|
✗ |
double valueByDofnsr = 1.49; |
| 304 |
|
✗ |
double valueByDofjsr = 1.49; |
| 305 |
|
✗ |
double valueByDofcsqn = 6.51; |
| 306 |
|
|
|
| 307 |
|
✗ |
m_m.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 308 |
|
✗ |
m_m.set(valueByDofm); |
| 309 |
|
✗ |
m_h.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 310 |
|
✗ |
m_h.set(valueByDofh); |
| 311 |
|
✗ |
m_j.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 312 |
|
✗ |
m_j.set(valueByDofj); |
| 313 |
|
✗ |
m_ao.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 314 |
|
✗ |
m_ao.set(valueByDofao); |
| 315 |
|
✗ |
m_io.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 316 |
|
✗ |
m_io.set(valueByDofio); |
| 317 |
|
✗ |
m_ua.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 318 |
|
✗ |
m_ua.set(valueByDofua); |
| 319 |
|
✗ |
m_ui.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 320 |
|
✗ |
m_ui.set(valueByDofui); |
| 321 |
|
✗ |
m_xr.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 322 |
|
✗ |
m_xr.set(valueByDofxr); |
| 323 |
|
✗ |
m_xs.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 324 |
|
✗ |
m_xs.set(valueByDofxs); |
| 325 |
|
✗ |
m_d.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 326 |
|
✗ |
m_d.set(valueByDofd); |
| 327 |
|
✗ |
m_f.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 328 |
|
✗ |
m_f.set(valueByDoff); |
| 329 |
|
✗ |
m_fca.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 330 |
|
✗ |
m_fca.set(valueByDoffca); |
| 331 |
|
✗ |
m_urel.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 332 |
|
✗ |
m_urel.set(0.); |
| 333 |
|
✗ |
m_vrel.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 334 |
|
✗ |
m_vrel.set(valueByDofvrel); |
| 335 |
|
✗ |
m_wrel.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 336 |
|
✗ |
m_wrel.set(valueByDofwrel); |
| 337 |
|
✗ |
m_nai.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 338 |
|
✗ |
m_nai.set(valueByDofnai); |
| 339 |
|
✗ |
m_nao.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 340 |
|
✗ |
m_nao.set(valueByDofnao); |
| 341 |
|
✗ |
m_cao.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 342 |
|
✗ |
m_cao.set(valueByDofcao); |
| 343 |
|
✗ |
m_ki.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 344 |
|
✗ |
m_ki.set(valueByDofki); |
| 345 |
|
✗ |
m_ko.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 346 |
|
✗ |
m_ko.set(valueByDofko); |
| 347 |
|
✗ |
m_cai.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 348 |
|
✗ |
m_cai.set(valueByDofcai); |
| 349 |
|
✗ |
m_naiont.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 350 |
|
✗ |
m_naiont.set(0.); |
| 351 |
|
✗ |
m_kiont.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 352 |
|
✗ |
m_kiont.set(0.); |
| 353 |
|
✗ |
m_caiont.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 354 |
|
✗ |
m_caiont.set(0.); |
| 355 |
|
✗ |
m_ileak.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 356 |
|
✗ |
m_ileak.set(0.); |
| 357 |
|
✗ |
m_iup.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 358 |
|
✗ |
m_iup.set(0.); |
| 359 |
|
✗ |
m_itr.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 360 |
|
✗ |
m_itr.set(0.); |
| 361 |
|
✗ |
m_irel.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 362 |
|
✗ |
m_irel.set(0.); |
| 363 |
|
✗ |
m_cmdn.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 364 |
|
✗ |
m_cmdn.set(valueByDofcmdn); |
| 365 |
|
✗ |
m_trpn.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 366 |
|
✗ |
m_trpn.set(valueByDoftrpn); |
| 367 |
|
✗ |
m_nsr.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 368 |
|
✗ |
m_nsr.set(valueByDofnsr); |
| 369 |
|
✗ |
m_jsr.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 370 |
|
✗ |
m_jsr.set(valueByDofjsr); |
| 371 |
|
✗ |
m_csqn.duplicateFrom(m_linearProblemBidomainCurv[iProblem]->vector()); |
| 372 |
|
✗ |
m_csqn.set(valueByDofcsqn); |
| 373 |
|
|
} |
| 374 |
|
|
|
| 375 |
|
|
//Debug print. |
| 376 |
|
✗ |
if(m_verbose > 10) { |
| 377 |
|
✗ |
PetscPrintf(MpiInfo::petscComm(),"\n\t\t m_W_0 (==m_solEDO (ionicSolver) at time == 0):"); |
| 378 |
|
✗ |
m_W_0.view(); |
| 379 |
|
|
} |
| 380 |
|
|
|
| 381 |
|
|
|
| 382 |
|
|
// Read fibers only for testCase == 1. |
| 383 |
|
✗ |
if (FelisceParam::instance().testCase == 1) { |
| 384 |
|
✗ |
m_linearProblemBidomainCurv[iProblem]->readData(*io()); |
| 385 |
|
|
} |
| 386 |
|
|
|
| 387 |
|
|
//Initialize heterogeneous parameters for schaf and courtemanche solvers. |
| 388 |
|
✗ |
if (FelisceParam::instance().typeOfIonicModel == "schaf") { |
| 389 |
|
✗ |
initializeSchafParameter(); |
| 390 |
|
|
} |
| 391 |
|
✗ |
if (FelisceParam::instance().typeOfIonicModel == "fhn") { |
| 392 |
|
✗ |
initializeFhNParameter(); |
| 393 |
|
✗ |
} else if (FelisceParam::instance().typeOfIonicModel == "court") { |
| 394 |
|
✗ |
initializeCourtParameter(); |
| 395 |
|
|
} |
| 396 |
|
|
} |
| 397 |
|
|
|
| 398 |
|
✗ |
void BidomainCurvModel::postAssemblingMatrixRHS(std::size_t iProblem) { |
| 399 |
|
✗ |
evalIapp(); |
| 400 |
|
✗ |
if (FelisceParam::instance().hasAppliedExteriorCurrent) |
| 401 |
|
✗ |
evalIappExt(); |
| 402 |
|
✗ |
finalizeRHSDP(iProblem); |
| 403 |
|
|
// Calculate m_RHS = mass * RHS. |
| 404 |
|
✗ |
m_linearProblemBidomainCurv[iProblem]->addMatrixRHS(); |
| 405 |
|
|
} |
| 406 |
|
|
|
| 407 |
|
✗ |
void BidomainCurvModel::initializeSchafParameter() { |
| 408 |
|
|
// Initialize TauClose. |
| 409 |
|
✗ |
m_schaf->fctTauClose().initialize(m_fstransient); |
| 410 |
|
✗ |
if (FelisceParam::instance().hasHeteroTauClose) { |
| 411 |
|
✗ |
m_linearProblemBidomainCurv[0]->evalFunctionOnDof(m_schaf->fctTauClose(), m_schaf->tauClose()); |
| 412 |
|
|
} |
| 413 |
|
|
// Initialize TauOut : heterogeneous in case of infarct. |
| 414 |
|
✗ |
m_schaf->fctTauOut().initialize(m_fstransient); |
| 415 |
|
✗ |
if (FelisceParam::instance().hasInfarct) { |
| 416 |
|
✗ |
m_linearProblemBidomainCurv[0]->evalFunctionOnDof(m_schaf->fctTauOut(), m_schaf->tauOut()); |
| 417 |
|
|
} |
| 418 |
|
|
} |
| 419 |
|
|
|
| 420 |
|
✗ |
void BidomainCurvModel::initializeFhNParameter() { |
| 421 |
|
✗ |
if (FelisceParam::instance().hasInfarct) { |
| 422 |
|
✗ |
m_fhn->fctSpar().initialize(m_fstransient); |
| 423 |
|
✗ |
m_linearProblemBidomainCurv[0]->evalFunctionOnDof(m_fhn->fctSpar(), m_fhn->f0Par()); |
| 424 |
|
|
} |
| 425 |
|
|
} |
| 426 |
|
|
|
| 427 |
|
✗ |
void BidomainCurvModel::initializeCourtParameter() { |
| 428 |
|
|
// Initialize gToMax |
| 429 |
|
✗ |
m_court->fctCourtCondIto().initialize(m_fstransient); |
| 430 |
|
|
// Initialize gCaLMax |
| 431 |
|
✗ |
m_court->fctCourtCondICaL().initialize(m_fstransient); |
| 432 |
|
✗ |
if (FelisceParam::instance().hasHeteroCourtPar) { |
| 433 |
|
✗ |
m_linearProblemBidomainCurv[0]->evalFunctionOnDof(m_court->fctCourtCondIto(), m_court->courtCondIto()); |
| 434 |
|
✗ |
m_linearProblemBidomainCurv[0]->evalFunctionOnDof(m_court->fctCourtCondICaL(), m_court->courtCondICaL()); |
| 435 |
|
|
} |
| 436 |
|
✗ |
if (!FelisceParam::instance().hasHeteroCondAtria) { |
| 437 |
|
|
// Initialize multiplicative coefficient |
| 438 |
|
✗ |
m_court->fctCourtCondMultCoeff().initialize(m_fstransient); |
| 439 |
|
|
// Warning: extraData m_linearProblemBidomainCurv[0]->Reference() size has to be numDof (not number of mesh points). |
| 440 |
|
✗ |
m_linearProblemBidomainCurv[0]->evalFunctionOnDof(m_court->fctCourtCondMultCoeff(), m_court->courtCondMultCoeff(), m_linearProblemBidomainCurv[0]->Reference()); |
| 441 |
|
|
} |
| 442 |
|
|
} |
| 443 |
|
|
|
| 444 |
|
|
// Pay attention on the call of this : |
| 445 |
|
|
// call BidomainModel::writeSolution() function instead of (non-virtual) Model::writeSolution() function |
| 446 |
|
✗ |
void BidomainCurvModel::writeSolution() { |
| 447 |
|
✗ |
if (MpiInfo::rankProc() == 0) { |
| 448 |
|
✗ |
if (m_meshIsWritten == false) writeMesh(); |
| 449 |
|
|
} |
| 450 |
|
|
|
| 451 |
|
✗ |
if( (m_fstransient->iteration % FelisceParam::instance().frequencyWriteSolution == 0) or m_hasFinished) { |
| 452 |
|
✗ |
if(FelisceParam::verbose() > 1) PetscPrintf(MpiInfo::petscComm(),"Write solutions\n"); |
| 453 |
|
✗ |
for (std::size_t ipb = 0; ipb < m_linearProblem.size(); ipb++) { |
| 454 |
|
|
|
| 455 |
|
✗ |
m_linearProblemBidomainCurv[ipb]->writeSolution(MpiInfo::rankProc(), m_ios, m_fstransient->time, m_fstransient->iteration); |
| 456 |
|
|
|
| 457 |
|
✗ |
if(FelisceParam::instance().printIonicVar) { |
| 458 |
|
|
int rankProc; |
| 459 |
|
✗ |
MPI_Comm_rank(MpiInfo::petscComm(),&rankProc); |
| 460 |
|
✗ |
if ( m_fstransient->iteration == 0 ) { |
| 461 |
|
✗ |
double * ionicSolToSave = new double[m_linearProblemBidomainCurv[ipb]->numDofPerUnknown(0)]; |
| 462 |
|
✗ |
m_linearProblemBidomainCurv[ipb]->fromVecToDoubleStar(ionicSolToSave, m_W_0, rankProc, 1, m_linearProblemBidomainCurv[ipb]->numDofPerUnknown(0)); |
| 463 |
|
✗ |
if (rankProc == 0) { |
| 464 |
|
✗ |
m_linearProblemBidomainCurv[ipb]->writeEnsightScalar(ionicSolToSave, static_cast<int>(m_fstransient->iteration/FelisceParam::instance().frequencyWriteSolution), "ionicVar"); |
| 465 |
|
✗ |
m_linearProblemBidomainCurv[ipb]->writeEnsightCase(static_cast<int>(m_fstransient->iteration/FelisceParam::instance().frequencyWriteSolution)+1,"ionicVar"); |
| 466 |
|
|
} |
| 467 |
|
✗ |
delete [] ionicSolToSave; |
| 468 |
|
|
|
| 469 |
|
|
} else { |
| 470 |
|
✗ |
double * ionicSolToSave = new double[m_linearProblemBidomainCurv[ipb]->numDofPerUnknown(0)]; |
| 471 |
|
✗ |
m_linearProblemBidomainCurv[ipb]->fromVecToDoubleStar(ionicSolToSave, m_ionic->sol(), rankProc, 1, m_linearProblemBidomainCurv[ipb]->numDofPerUnknown(0)); |
| 472 |
|
✗ |
if (rankProc == 0) { |
| 473 |
|
✗ |
m_linearProblemBidomainCurv[ipb]->writeEnsightScalar(ionicSolToSave, static_cast<int>(m_fstransient->iteration/FelisceParam::instance().frequencyWriteSolution), "ionicVar"); |
| 474 |
|
✗ |
m_linearProblemBidomainCurv[ipb]->writeEnsightCase(static_cast<int>(m_fstransient->iteration/FelisceParam::instance().frequencyWriteSolution)+1,"ionicVar"); |
| 475 |
|
|
} |
| 476 |
|
✗ |
delete [] ionicSolToSave; |
| 477 |
|
|
} |
| 478 |
|
|
} |
| 479 |
|
✗ |
if (MpiInfo::rankProc() == 0) { |
| 480 |
|
✗ |
for(std::size_t iio=0; iio<m_ios.size(); ++iio) { |
| 481 |
|
✗ |
if ( m_ios[iio]->typeOutput == 1 ) // 1 : ensight{ |
| 482 |
|
✗ |
m_ios[iio]->postProcess(m_fstransient->time/*, !m_sameGeometricMeshForVariable*/); |
| 483 |
|
|
} |
| 484 |
|
|
} |
| 485 |
|
|
} |
| 486 |
|
|
} |
| 487 |
|
|
} |
| 488 |
|
|
|
| 489 |
|
✗ |
void BidomainCurvModel::forward() { |
| 490 |
|
|
//Write solution with ensight. |
| 491 |
|
✗ |
BidomainCurvModel::writeSolution(); |
| 492 |
|
|
//Advance time step. |
| 493 |
|
✗ |
updateTime(FlagMatrixRHS::only_rhs); |
| 494 |
|
✗ |
printNewTimeIterationBanner(); |
| 495 |
|
|
|
| 496 |
|
✗ |
if ( m_fstransient->iteration == 1) { |
| 497 |
|
✗ |
m_bdfEdp.initialize(m_linearProblemBidomainCurv[0]->solution()); |
| 498 |
|
✗ |
m_linearProblemBidomainCurv[0]->initializeTimeScheme(&m_bdfEdp); |
| 499 |
|
|
//m_extrapolate = initial solution. |
| 500 |
|
✗ |
m_bdfEdp.extrapolate(m_extrapolate); |
| 501 |
|
|
|
| 502 |
|
✗ |
if (FelisceParam::instance().typeOfIonicModel == "court") { |
| 503 |
|
✗ |
m_court->defineSizeAndMappingOfIonicProblem(m_linearProblemBidomainCurv[0]->numDofLocalPerUnknown(potTransMemb), m_linearProblemBidomainCurv[0]->mappingDofLocalToDofGlobal(potTransMemb), m_linearProblemBidomainCurv[0]->ao()); |
| 504 |
|
✗ |
m_court->initializeExtrap(m_extrapolate); |
| 505 |
|
✗ |
m_court->initializeConcentrationsAndGateConditions(m_m, m_h, m_j, m_ao, m_io, m_ua, m_ui, m_xr, m_xs, m_d, m_f, m_fca, m_urel, m_vrel, m_wrel, m_nai, m_nao, m_cao, m_ki, m_ko, m_cai, m_naiont, m_kiont, m_caiont, m_ileak, m_iup, m_itr, m_irel, m_cmdn, m_trpn, m_nsr, m_jsr, m_csqn); |
| 506 |
|
✗ |
m_buildCourt = true; |
| 507 |
|
|
} |
| 508 |
|
|
else { |
| 509 |
|
✗ |
m_ionic->defineSizeAndMappingOfIonicProblem(m_linearProblemBidomainCurv[0]->numDofLocalPerUnknown(potTransMemb), m_linearProblemBidomainCurv[0]->mappingDofLocalToDofGlobal(potTransMemb), m_linearProblemBidomainCurv[0]->ao()); |
| 510 |
|
✗ |
m_ionic->initializeExtrap(m_extrapolate); |
| 511 |
|
✗ |
m_ionic->initialize(m_W_0); |
| 512 |
|
✗ |
m_buildIonic = true; |
| 513 |
|
|
} |
| 514 |
|
✗ |
if (FelisceParam::instance().dataAssimilation) { |
| 515 |
|
✗ |
m_linearProblemBidomainCurv[0]->gatherSolution(); |
| 516 |
|
✗ |
m_linearProblemBidomainCurv[0]->initSolutionTimeBef(); |
| 517 |
|
✗ |
m_linearProblemBidomainCurv[0]->readDataForDA(*io(),m_fstransient->iteration); |
| 518 |
|
✗ |
m_linearProblemBidomainCurv[0]->initLevelSet(); |
| 519 |
|
✗ |
m_linearProblemBidomainCurv[0]->levelSet(FelisceParam::instance().minLSPotTM,FelisceParam::instance().maxLSPotTM); |
| 520 |
|
|
} |
| 521 |
|
|
} |
| 522 |
|
|
else { |
| 523 |
|
✗ |
m_bdfEdp.update(m_linearProblemBidomainCurv[0]->solution()); |
| 524 |
|
✗ |
m_bdfEdp.extrapolate(m_extrapolate); |
| 525 |
|
✗ |
if (FelisceParam::instance().typeOfIonicModel == "court") { |
| 526 |
|
✗ |
m_court->updateExtrap(m_extrapolate); |
| 527 |
|
|
} |
| 528 |
|
|
else { |
| 529 |
|
✗ |
m_ionic->update(m_extrapolate); |
| 530 |
|
|
} |
| 531 |
|
|
} |
| 532 |
|
|
|
| 533 |
|
✗ |
if (FelisceParam::instance().dataAssimilation) { |
| 534 |
|
✗ |
m_linearProblemBidomainCurv[0]->gatherSolution(); |
| 535 |
|
✗ |
m_linearProblemBidomainCurv[0]->solutionTimeBef(); |
| 536 |
|
✗ |
m_linearProblemBidomainCurv[0]->readDataForDA(*io(),m_fstransient->iteration); |
| 537 |
|
✗ |
m_linearProblemBidomainCurv[0]->levelSet(FelisceParam::instance().minLSPotTM,FelisceParam::instance().maxLSPotTM); |
| 538 |
|
|
} |
| 539 |
|
|
|
| 540 |
|
✗ |
if (FelisceParam::instance().typeOfIonicModel == "court") { |
| 541 |
|
✗ |
m_court->computeIon(); |
| 542 |
|
|
} |
| 543 |
|
|
else { |
| 544 |
|
✗ |
m_ionic->computeRHS(); |
| 545 |
|
✗ |
m_ionic->solveEDO(); |
| 546 |
|
✗ |
m_ionic->computeIon(); |
| 547 |
|
✗ |
m_ionic->updateBdf(); |
| 548 |
|
|
} |
| 549 |
|
|
|
| 550 |
|
✗ |
m_bdfEdp.computeRHSTime(m_fstransient->timeStep); |
| 551 |
|
|
|
| 552 |
|
|
//double timeDA =fmod(m_fstransient->iteration,1); |
| 553 |
|
|
|
| 554 |
|
|
// Assemble Matrix of linearProblem. |
| 555 |
|
✗ |
if ( m_fstransient->iteration == 1 ) { |
| 556 |
|
✗ |
m_linearProblemBidomainCurv[0]->assembleMatrixRHSBD(MpiInfo::rankProc()); |
| 557 |
|
✗ |
} else if (FelisceParam::instance().dataAssimilation) { //&&(timeDA == 0)) |
| 558 |
|
✗ |
m_linearProblemBidomainCurv[0]->assembleMatrixRHSBD(MpiInfo::rankProc(), FlagMatrixRHS::only_rhs); |
| 559 |
|
|
} |
| 560 |
|
|
|
| 561 |
|
|
//Specific operations before solve the system : add static matrix _Matrix[1] to the dynamic matrix of the system _Matrix. |
| 562 |
|
✗ |
postAssemblingMatrixRHS(); |
| 563 |
|
✗ |
m_linearProblemBidomainCurv[0]->solve(MpiInfo::rankProc(), MpiInfo::numProc()); |
| 564 |
|
|
|
| 565 |
|
|
} |
| 566 |
|
|
} |
| 567 |
|
|
|